All Classes Namespaces Functions Variables Typedefs Enumerations Enumerator Friends Pages
CustomManyParticleForceImpl.h
#ifndef OPENMM_CUSTOMMANYPARTICLEFORCEIMPL_H_
#define OPENMM_CUSTOMMANYPARTICLEFORCEIMPL_H_
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "ForceImpl.h"
#include "openmm/CustomManyParticleForce.h"
#include "openmm/Kernel.h"
#include "lepton/CustomFunction.h"
#include "lepton/ExpressionTreeNode.h"
#include "lepton/ParsedExpression.h"
#include <utility>
#include <map>
#include <string>
namespace OpenMM {
class OPENMM_EXPORT CustomManyParticleForceImpl : public ForceImpl {
public:
CustomManyParticleForceImpl(const CustomManyParticleForce& owner);
~CustomManyParticleForceImpl();
void initialize(ContextImpl& context);
const CustomManyParticleForce& getOwner() const {
return owner;
}
void updateContextState(ContextImpl& context) {
// This force field doesn't update the state directly.
}
double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups);
std::map<std::string, double> getDefaultParameters();
std::vector<std::string> getKernelNames();
void updateParametersInContext(ContextImpl& context);
static Lepton::ParsedExpression prepareExpression(const CustomManyParticleForce& force, const std::map<std::string, Lepton::CustomFunction*>& functions, std::map<std::string, std::vector<int> >& distances,
std::map<std::string, std::vector<int> >& angles, std::map<std::string, std::vector<int> >& dihedrals);
static void buildFilterArrays(const CustomManyParticleForce& force, int& numTypes, std::vector<int>& particleTypes, std::vector<int>& orderIndex, std::vector<std::vector<int> >& particleOrder);
private:
class FunctionPlaceholder;
static Lepton::ExpressionTreeNode replaceFunctions(const Lepton::ExpressionTreeNode& node, std::map<std::string, int> atoms,
std::map<std::string, std::vector<int> >& distances, std::map<std::string, std::vector<int> >& angles,
std::map<std::string, std::vector<int> >& dihedrals);
static void generatePermutations(std::vector<int>& values, int numFixed, std::vector<std::vector<int> >& result);
const CustomManyParticleForce& owner;
Kernel kernel;
};
} // namespace OpenMM
#endif /*OPENMM_CUSTOMMANYPARTICLEFORCEIMPL_H_*/
OpenMM::ContextImpl
This is the internal implementation of a Context.
Definition: ContextImpl.h:53
OpenMM::CustomManyParticleForceImpl::getOwner
const CustomManyParticleForce & getOwner() const
Get the Force object from which this ForceImpl was created.
Definition: CustomManyParticleForceImpl.h:56
OpenMM::CustomManyParticleForceImpl::updateContextState
void updateContextState(ContextImpl &context)
This method is called at the beginning of each time step.
Definition: CustomManyParticleForceImpl.h:59
OpenMM::Kernel
A Kernel encapsulates a particular implementation of a calculation that can be performed on the data ...
Definition: Kernel.h:58
OpenMM::ForceImpl
A ForceImpl provides the internal implementation of a Force.
Definition: ForceImpl.h:57
OpenMM::CustomManyParticleForce
This class supports a wide variety of nonbonded N-particle interactions, where N is user specified...
Definition: CustomManyParticleForce.h:162
OpenMM::CustomManyParticleForceImpl
This is the internal implementation of CustomManyParticleForce.
Definition: CustomManyParticleForceImpl.h:51